MDDB_Tutorials/example_inputs.yaml at main · PDNALab/MDDB_Tutorials · GitHub

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authors:
- Imesh Ranaweera
- Alberto Perez
boxtype: None
cg_selection: []
chainnames: []
citation: null
collections: []
contact: For any questions please send a mail to perez@chem.ufl.edu
customs: []
cv19_abs: ''
cv19_nanobs: ''
cv19_startconf: ''
cv19_unit: ''
description: Replica-exchange MELD simulation of Protein G to study its folding pathway
  using Grappa force field.
ensemble: NPT
ff:
- Grappa
- Amber ff14SB
forced_references: []
framestep: 0.02855
groups:
- Perez Lab UF
input_topology_filepath: raw/topology.prmtop
interactions: []
license: Creative Commons Attribution 4.0 International Public License
ligands: []
linkcense: https://creativecommons.org/licenses/by/4.0/
links:
- name: Navigate to FoldBind Data Set for more information.
  url: https://github.com/PDNALab/FoldBindDataset
mdref: 0
mds:
- input_structure_filepath: /orange/alberto.perezant-mddb/MDDB/3GB1/raw/structure.pdb
  input_trajectory_filepaths:
  - /orange/alberto.perezant-mddb/MDDB/3GB1/raw/trajectory.29.dcd
  mdir: replica_0
  name: Replica 0
  temp: 300
- mdir: replica_1
  name: Replica 1
  temp: 321.65
- mdir: replica_2
  name: Replica 2
  temp: 344.85
- mdir: replica_3
  name: Replica 3
  temp: 369.74
- mdir: replica_4
  name: Replica 4
  temp: 396.42
- mdir: replica_5
  name: Replica 5
  temp: 425.02
- mdir: replica_6
  name: Replica 6
  temp: 455.69
- mdir: replica_7
  name: Replica 7
  temp: 488.57
- mdir: replica_8
  name: Replica 8
  temp: 523.82
- mdir: replica_9
  name: Replica 9
  temp: 550
- mdir: replica_10
  name: Replica 10
  temp: 550
- mdir: replica_11
  name: Replica 11
  temp: 550
- mdir: replica_12
  name: Replica 12
  temp: 550
- mdir: replica_13
  name: Replica 13
  temp: 550
- mdir: replica_14
  name: Replica 14
  temp: 550
- mdir: replica_15
  name: Replica 15
  temp: 550
- mdir: replica_16
  name: Replica 16
  temp: 550
- mdir: replica_17
  name: Replica 17
  temp: 550
- mdir: replica_18
  name: Replica 18
  temp: 550
- mdir: replica_19
  name: Replica 19
  temp: 550
- mdir: replica_20
  name: Replica 20
  temp: 550
- mdir: replica_21
  name: Replica 21
  temp: 550
- mdir: replica_22
  name: Replica 22
  temp: 550
- mdir: replica_23
  name: Replica 23
  temp: 550
- mdir: replica_24
  name: Replica 24
  temp: 550
- mdir: replica_25
  name: Replica 25
  temp: 550
- mdir: replica_26
  name: Replica 26
  temp: 550
- mdir: replica_27
  name: Replica 27
  temp: 550
- mdir: replica_28
  name: Replica 28
  temp: 550
- mdir: replica_29
  name: Replica 29
  temp: 550
- mdir: replica_00
  name: replica 00
- mdir: replica_01
  name: replica 01
- mdir: replica_02
  name: replica 02
- mdir: replica_03
  name: replica 03
- mdir: replica_04
  name: replica 04
- mdir: replica_05
  name: replica 05
- mdir: replica_06
  name: replica 06
- mdir: replica_07
  name: replica 07
- mdir: replica_08
  name: replica 08
- mdir: replica_09
  name: replica 09
method: Replica Exchange Molecular Dynamics
multimeric: []
name: MELD simulation for protein G (3GB1) using Grappa force field.
orientation: null
pbc_selection: auto
pdb_ids:
- 3GB1
program: MELD
temp: 300
thanks: We would like to thank our funder, National Science Foundation (NSF) and HiPerGator
  3.0 for the computational resources.
timestep: 2
type: trajectory
version: 0.6.1
wat: null